Hello! Thank you for the query. Such symptoms may be caused by kidney problem, especially by chronic kidney disease. There is a possibility that kidney stones can cause renal failure due to urine flow blockage. It causes slow renal degeneration and results with blood intoxication what leads to stubborn headaches, severe fatigue and many many other symptoms. But stones should be present in both kidneys to cause this condition. So it is suggested for you to have fool blood work with creatinine level. The other reason of headaches can be simple fever due to urinary tract infection. It should be associated with frequent urinating, burning when urinating and frequent urinating. Urine analysis should be performed as well. Hope this will help. Regards.